The Uighurs had applied for asylum at the United Nations refugee office, after fleeing riots that killed about 200 people in southern China in July.
"This group will be particularly vulnerable to torture. Because of those concerns, Cambodia shouldn't send them back"
The UN had urged Cambodia to stop the deportation. A spokeswoman for the UN refugee agency said it had not finished evaluating the Uighurs, including two children, for refugee status.
Human rights groups say they fear for the lives of Uighurs deported to China.
"It is hugely concerning that Cambodian authorities are not giving this group an opportunity to seek asylum, or for authorities to assess their asylum case," Brittis Edman, a Cambodia researcher with Amnesty International, said, before the expulsion.
"This group will be particularly vulnerable to torture. Because of those concerns, Cambodia shouldn't send them back."
The deportation comes a day before Xi Jinping, the Chinese vice-president, visits Cambodia as part of a four-country tour.
Cambodia has been under pressure from China, which has called the Uighurs "criminals" after they fled the country.
Uighurs say Beijing has long restricted their rights, particularly clamping down on their practise of Islam.
Tensions between majority Han Chinese and the Turkic Uighurs in their traditional homeland in western China exploded into rioting in July.
The violence started with protests against attacks on Uighur workers.
The Chinese government have said that nearly 200 people, mostly Han Chinese, died in the unrest.
At least eight people have been sentenced to death for murder and other crimes during the rioting, and nine other people have been executed, Chinese state media has reported.